[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [modeller_usage] modeling of phosphorylated polypeptide

Dibyabhaba Pradhan wrote:
> I modelled number of proteins by basic modelling. After basic
> modelling during procheck evaluation the residues in most favorable
> region is generally above 90% but after loop refinement the residues
> in most favorable region comes below 90%. Please kindly inform me what
> may be the region for this.
> 
> Also after energy minimization the the percentage of residue in most
> favorable region decreses.

I'm not sure what this has to do with phosphorylation, but there is
certainly no guarantee that a single minimization will give a "better"
model. You'd be better off building several models to get a reasonable
sampling of the energy landscape and then picking the best cluster or
single model.

	Ben Webb, Modeller Caretaker
-- 
             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage